Joyous shouts of "Allahu akbar" echoed across the headquarters of the Philippines' biggest Muslim rebel group as a pact to end four decades of bloodshed was signed, but there were also fears war clouds had yet to pass.

The Moro Islamic Liberation Front (MILF) ended its rebellion on Thursday when its leaders signed a deal in Manila with the government that would create a new, autonomous Muslim homeland in the southern Philippines.

Various armed Muslim groups have been fighting since the 1970s for an independent Islamic state or autonomous rule in the south, which they regard as their ancestral home, and the conflict has claimed tens of thousands of lives.

MILF leader Murad Ebrahim said at the signing ceremony the accord was the "crowning glory" of his organisation's struggle, and his troops at their main camp 900 kilometres (550 miles) to the south voiced similar jubilation.

Hundreds of rebels, wearing camouflage uniforms and pointing assault rifles to the sky, shouted "Allahu akbar", or "God is greater", as they watched the historic moment on a television screen in a grassy field.

Senior MILF commander Usop Pasigan, 65, said he took up arms at the age of 17 and had lost three brothers in the fighting. Now he just wants to be a farmer and for his son to be able to live a normal life.

"I hope my boy will be able to finish college and not be an MILF fighter, like me," Pasigan told AFP as he stood alongside many other elderly soldiers in their military fatigues.

For Jamira Mapagkasunggot, 56, a member of the MILF women's auxiliary battalion, peace would mean being able to live without the constant fear of death.

"Most of the women have lost a father, a son or a nephew," she told AFP at Camp Darapanan, where rebels and their families live inside a sprawling compound of coconut groves and corn fields.

- Fears of more conflict -

But while Mapagkasunggot was optimistic about the process, she also acknowledged the many potential pitfalls that lay ahead.

"We fear some groups might not be supportive of these peace talks," she said, referring to a wide range of smaller armed groups that roam the impoverished and often lawless southern Philippines that are opposed to the peace process.

Among them is the Bangsamoro Islamic Freedom Fighters (BIFF), which split from the MILF in 2008 because it wanted to continue pursuing independence.

The BIFF has just a few hundred militants, according to the military, but it has launched deadly attacks in the past to disrupt the peace process and has been able to withstand repeated government assaults against it.

"The war is not yet over. We are still here," BIFF spokesman Abu Missry Mama told AFP by telephone from his secret base elsewhere in the south.

Another armed group not covered by the peace accord is the Al-Qaeda-linked Abu Sayyaf, which specialises in kidnapping for ransom, while the area is plagued by private armies of corrupt politicians who may resist the new government.

The MILF, which has about 10,000 fighters, has committed to working with the government to neutralise the threat of rogue groups such as the BIFF, meaning future battles against former comrades are possible.

- Accord faces hurdles -

Meanwhile, there are doubts President Benigno Aquino's administration will be able to fulfil its commitments in the accord.

Among the hurdles is securing approval from Congress for a "Basic Law" that would create the autonomous region.

Without the law, the autonomous region cannot exist, but there are no guarantees that Aquino can secure majority support in Congress for the highly sensitive issue.

As insurance, the MILF has said it will not reveal to the government the names of its fighters, or hand over its giant arsenal of weapons, until the law is passed and the autonomous region created.

The MILF leadership is also aware that other peace efforts have failed, leading to more conflict.

In 1996, another major rebel group, the Moro National Liberation Front (MNLF), signed a peace deal with the government in return for the creation of a Muslim autonomous area.

But critics, including the MILF, said the autonomous area did not give Muslims enough powers.

Under the new peace deal, the new autonomous region would replace the old one, angering factions of the MNLF and opening another potential front for conflict.

MNLF founder Nur Misuari's followers attacked the southern port city of Zamboanga in September last year in an effort to derail the peace talks.

The military responded with an unrelenting assault in which more than 100 MNLF fighters were killed.

In a speech at the signing ceremony, Aquino cited the September clashes as he warned he was prepared to unleash his troops on any armed group opposed to the peace process.

"Those who want to test the resolve of the state will be met with a firm response based on righteousness and justice, as we demonstrated in Zamboanga," Aquino said.

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